def relate_structures(cfg,log,db, pm):
try:
log.info('Merging Training and Result Sets...')
rows = db.getData(cfg.sqlCopyTrainingSetIntoLiterature).fetchall()
for row in rows:
article = pm.get_pubmed_article(row['pubmed_id'])
pm.save_pubmed_article(row['pubmed_id'], article, 'Literature')
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateRel)
candidates = db.getData(cfg.sqlSelectCandidates).fetchall()
for addFile in candidates:
key = addFile['pdbID']
f = PDB.parse_prody(cfg,key)
if f.journal.pmid != "":
db.executeCommand(cfg.sqlInsertRel, (addFile['pdbID'], f.journal.pmid, 'Originator'))
log.info('Opening article to find references to structures...')
fileName = pm.get_related_pubmed_articles(f.journal.pmid)
for item in fileName[0]['LinkSetDb'][0]['Link']:
db.executeCommand(cfg.sqlInsertRel, (addFile['pdbID'], item['Id'], 'Related'))
db.commit()
except:
db.rollback()
log.error(traceback.format_exc())
raise Exception('Training Set was not built.')
def relate_structures(cfg, log, db, pm):
try:
log.info('Merging Training and Result Sets...')
rows = db.getData(cfg.sqlCopyTrainingSetIntoLiterature).fetchall()
for row in rows:
article = pm.get_pubmed_article(row['pubmed_id'])
pm.save_pubmed_article(row['pubmed_id'], article, 'Literature')
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateRel)
candidates = db.getData(cfg.sqlSelectCandidates).fetchall()
for addFile in candidates:
key = addFile['pdbID']
f = PDB.parse_prody(cfg, key)
if f.journal.pmid != "":
db.executeCommand(
cfg.sqlInsertRel,
(addFile['pdbID'], f.journal.pmid, 'Originator'))
log.info('Opening article to find references to structures...')
fileName = pm.get_related_pubmed_articles(f.journal.pmid)
for item in fileName[0]['LinkSetDb'][0]['Link']:
db.executeCommand(
cfg.sqlInsertRel,
(addFile['pdbID'], item['Id'], 'Related'))
db.commit()
except:
db.rollback()
log.error(traceback.format_exc())
raise Exception('Training Set was not built.')
def build_training_set(cfg, log, db, pm):
try:
listAdded = []
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateTrainingSet)
log.info('Getting Reference articles...')
candidates = db.getData(cfg.sqlSelectCandidates).fetchall()
for addFile in candidates:
key = addFile[0]
f = PDB.parse_prody(cfg, key)
if f.status == 'Imported' and (
f.journal.pmid not in listAdded) and f.journal.pmid != "":
article = pm.get_pubmed_article(f.journal.pmid)
pm.save_pubmed_article(f.journal.pmid, article, 'Training')
listAdded.append(f.journal.pmid)
db.commit()
except:
log.error(traceback.format_exc())
db.rollback()
raise Exception('Training Set was not built.')
try:
listAdded = []
<<<<<<< HEAD
=======
>>>>>>> origin/master
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateTrainingSet)
log.info('Getting Reference articles...')
candidates = db.getData(cfg.sqlSelectCandidates).fetchall()
for addFile in candidates:
key = addFile['pdbID']
f = PDB.parse_prody(cfg,key)
if (f.journal.pmid not in listAdded) and f.journal.pmid != "":
article = pm.get_pubmed_article(f.journal.pmid)
pm.save_pubmed_article(f.journal.pmid,article,'Training')
listAdded.append(f.journal.pmid)
db.commit()
except:
log.error(traceback.format_exc())
db.rollback()
raise Exception('Training Set was not built.')
def search_literature(cfg,log,db,pm):
try:
if cfg.FullReload:
db.executeCommand(cfg.sqlTruncateLiterature)
